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    ZNF419 zinc finger protein 419 [ Homo sapiens (human) ]

    Gene ID: 79744, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ZNF419provided by HGNC
    Official Full Name
    zinc finger protein 419provided by HGNC
    Primary source
    HGNC:HGNC:20648
    See related
    Ensembl:ENSG00000105136 MIM:617410; AllianceGenome:HGNC:20648
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ZAPHIR; ZNF419A
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 5.2), spleen (RPKM 4.2) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ZNF419 in Genome Data Viewer
    Location:
    19q13.43
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (57487750..57496098)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (60579865..60593144)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (57999118..58007466)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene vomeronasal 1 receptor 107 pseudogene Neighboring gene zinc finger protein 772 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:57988249-57989448 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:57998906-57999406 Neighboring gene zinc finger protein 773 Neighboring gene zinc finger protein 549

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. A polymorphism in the splice donor site of ZNF419 results in the novel renal cell carcinoma-associated minor histocompatibility antigen ZAPHIR. Broen K, et al. PLoS One, 2011. PMID 21738768, Free PMC Article
    2. Allele-specific splicing effects on DKKL1 and ZNF419 transcripts in HeLa cells. Martin G, et al. Gene, 2017 Jan 20. PMID 27826023
    3. Acetylation-Mimic Mutation of TRIM28-Lys304 to Gln Attenuates the Interaction with KRAB-Zinc-Finger Proteins and Affects Gene Expression in Leukemic K562 Cells. Chang YJ, et al. Int J Mol Sci, 2023 Jun 6. PMID 37372979, Free PMC Article
    4. Assessment of community efforts to advance network-based prediction of protein-protein interactions. Wang XW, et al. Nat Commun, 2023 Mar 22. PMID 36949045, Free PMC Article
    5. Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. Suzuki Y, et al. Genome Res, 2004 Sep. PMID 15342556, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. previously unreported alternative splicing patterns in the genes ZNF419 and DKKL1
      Title: Allele-specific splicing effects on DKKL1 and ZNF419 transcripts in HeLa cells.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ23233

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein 419
    Names
    zinc finger protein 419A

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_054882.1 RefSeqGene

      Range
      5040..13388
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001098491.2 → NP_001091961.1  zinc finger protein 419 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC003005, AK026886, BC024259, DB004191
      Consensus CDS
      CCDS54325.1
      UniProtKB/Swiss-Prot
      Q96HQ0
      Related
      ENSP00000388864.1, ENST00000424930.6
      Conserved Domains (5) summary
      smart00349
      Location:28 → 88
      KRAB; krueppel associated box
      COG5048
      Location:262 → 418
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:262 → 282
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:28 → 67
      KRAB; KRAB box
      pfam13465
      Location:330 → 355
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001098492.2 → NP_001091962.1  zinc finger protein 419 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC024259, DC315347
      Consensus CDS
      CCDS54327.1
      UniProtKB/Swiss-Prot
      Q96HQ0
      Related
      ENSP00000390916.1, ENST00000426954.6
      Conserved Domains (5) summary
      smart00349
      Location:15 → 75
      KRAB; krueppel associated box
      COG5048
      Location:249 → 405
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:249 → 269
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:15 → 54
      KRAB; KRAB box
      pfam13465
      Location:317 → 342
      zf-H2C2_2; Zinc-finger double domain

    3. NM_001098493.2 → NP_001091963.1  zinc finger protein 419 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC024259, DC392630
      Consensus CDS
      CCDS54328.1
      UniProtKB/Swiss-Prot
      Q96HQ0
      Related
      ENSP00000414709.2, ENST00000442920.6
      Conserved Domains (5) summary
      smart00349
      Location:14 → 74
      KRAB; krueppel associated box
      COG5048
      Location:248 → 404
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:248 → 268
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:14 → 53
      KRAB; KRAB box
      pfam13465
      Location:316 → 341
      zf-H2C2_2; Zinc-finger double domain

    4. NM_001098494.2 → NP_001091964.1  zinc finger protein 419 isoform 5

      See identical proteins and their annotated locations for NP_001091964.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (5) that is shorter than isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC024259
      Consensus CDS
      CCDS42637.1
      UniProtKB/Swiss-Prot
      Q96HQ0
      Related
      ENSP00000299860.9, ENST00000347466.10
      Conserved Domains (5) summary
      smart00349
      Location:28 → 69
      KRAB; krueppel associated box
      COG5048
      Location:229 → 385
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:229 → 249
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:28 → 67
      KRAB; KRAB box
      pfam13465
      Location:297 → 322
      zf-H2C2_2; Zinc-finger double domain

    5. NM_001098495.2 → NP_001091965.1  zinc finger protein 419 isoform 6

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks two alternate in-frame exons in the 5' coding region, compared to variant 1, resulting in an isoform (6) that is shorter than isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC024259, BP336834, DC407547
      UniProtKB/Swiss-Prot
      Q96HQ0
      Conserved Domains (5) summary
      smart00349
      Location:15 → 56
      KRAB; krueppel associated box
      COG5048
      Location:216 → 372
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:216 → 236
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:15 → 54
      KRAB; KRAB box
      pfam13465
      Location:284 → 309
      zf-H2C2_2; Zinc-finger double domain

    6. NM_001098496.2 → NP_001091966.1  zinc finger protein 419 isoform 7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) lacks two alternate in-frame exons and and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (7) that is shorter than isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC024259, DC315347, DC425209
      Consensus CDS
      CCDS46211.1
      UniProtKB/Swiss-Prot
      Q96HQ0
      Related
      ENSP00000392129.2, ENST00000415379.6
      Conserved Domains (5) summary
      smart00349
      Location:14 → 55
      KRAB; krueppel associated box
      COG5048
      Location:215 → 371
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:215 → 235
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:14 → 53
      KRAB; KRAB box
      pfam13465
      Location:283 → 308
      zf-H2C2_2; Zinc-finger double domain

    7. NM_001291743.2 → NP_001278672.1  zinc finger protein 419 isoform 8

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) uses an alternate in-frame splice site and lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (8) that is shorter than isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC008297, CT002615, DC315347
      UniProtKB/Swiss-Prot
      Q96HQ0
      Conserved Domains (5) summary
      smart00349
      Location:27 → 68
      KRAB; krueppel associated box
      COG5048
      Location:228 → 384
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:228 → 248
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:27 → 66
      KRAB; KRAB box
      pfam13465
      Location:296 → 321
      zf-H2C2_2; Zinc-finger double domain

    8. NM_001291744.2 → NP_001278673.1  zinc finger protein 419 isoform 9

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9) uses an alternate splice site and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, and it also lacks an in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (9) is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC008297, DA548110, DC315347
      UniProtKB/Swiss-Prot
      Q96HQ0
      Conserved Domains (3) summary
      COG5048
      Location:173 → 329
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:173 → 193
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:241 → 266
      zf-H2C2_2; Zinc-finger double domain

    9. NM_001291745.2 → NP_001278674.1  zinc finger protein 419 isoform 10

      Status: VALIDATED

      Description
      Transcript Variant: This variant (10) lacks an alternate in-frame exon in the 5' coding region, and it uses an alternate splice site in its 3' terminal exon and thus differs in the 3' coding region, compared to variant 1. The encoded isoform (10) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      BC008297, BF110540, DC315347
      UniProtKB/Swiss-Prot
      Q96HQ0
      Conserved Domains (2) summary
      smart00349
      Location:15 → 75
      KRAB; krueppel associated box
      pfam01352
      Location:15 → 54
      KRAB; KRAB box

    10. NM_024691.4 → NP_078967.3  zinc finger protein 419 isoform 2

      See identical proteins and their annotated locations for NP_078967.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC024259, BP336834
      Consensus CDS
      CCDS54326.1
      UniProtKB/Swiss-Prot
      B4DXU7, B4E348, B7ZA41, E9PCP4, E9PED0, E9PET3, E9PFX9, Q96HQ0, Q9H5P0
      Related
      ENSP00000221735.7, ENST00000221735.12
      Conserved Domains (5) summary
      smart00349
      Location:27 → 87
      KRAB; krueppel associated box
      COG5048
      Location:261 → 417
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:261 → 281
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:27 → 66
      KRAB; KRAB box
      pfam13465
      Location:329 → 354
      zf-H2C2_2; Zinc-finger double domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      57487750..57496098
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      60579865..60593144
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322177.1 → XP_054178152.1  zinc finger protein 419 isoform X3

    2. XM_054322176.1 → XP_054178151.1  zinc finger protein 419 isoform X3

    3. XM_054322178.1 → XP_054178153.1  zinc finger protein 419 isoform X4

    4. XM_054322175.1 → XP_054178150.1  zinc finger protein 419 isoform X2

    5. XM_054322174.1 → XP_054178149.1  zinc finger protein 419 isoform X1

    6. XM_054322179.1 → XP_054178154.1  zinc finger protein 419 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96HQ0.2 GenPept UniProtKB/Swiss-Prot:Q96HQ0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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